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An experimentally derived confidence score for binary protein-protein interactions

(2009) NATURE METHODS. 6(1). p.91-98
Author
Organization
Abstract
Information on protein-protein interactions is of central importance for many areas of biomedical research. At present no method exists to systematically and experimentally assess the quality of individual interactions reported in interaction mapping experiments. To provide a standardized confidence-scoring method that can be applied to tens of thousands of protein interactions, we have developed an interaction tool kit consisting of four complementary, high-throughput protein interaction assays. We benchmarked these assays against positive and random reference sets consisting of well documented pairs of interacting human proteins and randomly chosen protein pairs, respectively. A logistic regression model was trained using the data from these reference sets to combine the assay outputs and calculate the probability that any newly identified interaction pair is a true biophysical interaction once it has been tested in the tool kit. This general approach will allow a systematic and empirical assignment of confidence scores to all individual protein-protein interactions in interactome networks.
Keywords
SACCHAROMYCES-CEREVISIAE, INTERACTION NETWORK, INTERACTION DATABASE, MAMMALIAN-CELLS, MAP, 2-HYBRID, PREDICTION, UPDATE

Citation

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Chicago
Braun, Pascal, Murat Tasan, Matija Dreze, Miriam Barrios-Rodiles, Irma Lemmens, Haiyuan Yu, Julie M. Sahalie, et al. 2009. “An Experimentally Derived Confidence Score for Binary Protein-protein Interactions.” Nature Methods 6 (1): 91–98.
APA
Braun, P., Tasan, M., Dreze, M., Barrios-Rodiles, M., Lemmens, I., Yu, H., Sahalie, J. M., et al. (2009). An experimentally derived confidence score for binary protein-protein interactions. NATURE METHODS, 6(1), 91–98.
Vancouver
1.
Braun P, Tasan M, Dreze M, Barrios-Rodiles M, Lemmens I, Yu H, et al. An experimentally derived confidence score for binary protein-protein interactions. NATURE METHODS. LONDON N1 9XW, ENGLAND: NATURE PUBLISHING GROUP; 2009;6(1):91–8.
MLA
Braun, Pascal, Murat Tasan, Matija Dreze, et al. “An Experimentally Derived Confidence Score for Binary Protein-protein Interactions.” NATURE METHODS 6.1 (2009): 91–98. Print.
@article{539423,
  abstract     = {Information on protein-protein interactions is of central importance for many areas of biomedical research. At present no method exists to systematically and experimentally assess the quality of individual interactions reported in interaction mapping experiments. To provide a standardized confidence-scoring method that can be applied to tens of thousands of protein interactions, we have developed an interaction tool kit consisting of four complementary, high-throughput protein interaction assays. We benchmarked these assays against positive and random reference sets consisting of well documented pairs of interacting human proteins and randomly chosen protein pairs, respectively. A logistic regression model was trained using the data from these reference sets to combine the assay outputs and calculate the probability that any newly identified interaction pair is a true biophysical interaction once it has been tested in the tool kit. This general approach will allow a systematic and empirical assignment of confidence scores to all individual protein-protein interactions in interactome networks.},
  author       = {Braun, Pascal and Tasan, Murat and Dreze, Matija and Barrios-Rodiles, Miriam and Lemmens, Irma and Yu, Haiyuan and Sahalie, Julie M. and Murray, Ryan R. and Roncari, Luba and De Smet, Anne-Sophie and Venkatesan, Kavitha and Rual, Jean-Francois and Rual, Jean-Francois and Vandenhaute, Jean and Cusick,, Michael E. and Pawson, Tony and Hill, David E. and Tavernier, Jan and Wrana, Jeffrey L and Roth, Frederick P. and Vidal, Marc},
  issn         = {1548-7091},
  journal      = {NATURE METHODS},
  language     = {eng},
  number       = {1},
  pages        = {91--98},
  publisher    = {NATURE PUBLISHING GROUP},
  title        = {An experimentally derived confidence score for binary protein-protein interactions},
  url          = {http://dx.doi.org/10.1038/NMETH.1281},
  volume       = {6},
  year         = {2009},
}

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